X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=7bcb4e41185bfa2104b3ef29432db0af7cbe58a2;hb=b4f80c1d2be78a8743a408a2b6d462b07f9f71ff;hp=df65678912b1f3bd112e630b13ef934eebc5e219;hpb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index df65678..7bcb4e4 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -14,6 +14,18 @@
 
 #include "engine.hpp"
 
+/***********************************************************************/
+Engine::Engine(){
+	try {
+		cFactory = CommandFactory::getInstance();
+		mout = MothurOut::getInstance();
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "Engine", "Engine");
+		exit(1);
+	}
+}
+
 /***********************************************************************/
 
 InteractEngine::InteractEngine(string path){
@@ -21,19 +33,11 @@ InteractEngine::InteractEngine(string path){
 	globaldata = GlobalData::getInstance();
 	globaldata->argv = path;
 	
-	system("clear");
-//	char buffer = ' ';
-//	ifstream header("introtext.txt");
-//	while(!header.eof()){
-//		cout << buffer;
-//		buffer = header.get();
-//	}
 }
 
 /***********************************************************************/
 
-InteractEngine::~InteractEngine(){
-	}
+InteractEngine::~InteractEngine(){}
 
 /***********************************************************************/
 //This function allows the user to input commands one line at a time until they quit.
@@ -44,98 +48,130 @@ bool InteractEngine::getInput(){
 		string commandName = "";
 		string options = "";
 		int quitCommandCalled = 0;
-		//bool errorFree;
-		//ErrorCheck* errorCheckor = new ErrorCheck();
-		
-		cout << "mothur v.1.3.0" << endl;
-		cout << "Last updated: 5/29/2009" << endl << endl;
-		cout << "by" << endl;
-		cout << "Patrick D. Schloss" << endl << endl;
-		cout << "Department of Microbiology" << endl;
-		cout << "The University of Massachusetts" << endl;
-		cout << "pschloss@micro.umass.edu" << endl;
-		cout << "http://schloss.micro.umass.edu/mothur" << endl << endl << endl;
-		cout << "Distributed under the GNU General Public License" << endl << endl;
-		cout << "Type 'help()' for information on the commands that are available" << endl << endl;
-		cout << "Type 'quit()' to exit program" << endl;
-
+		
 		while(quitCommandCalled != 1){
 
-			cout << endl << "mothur > ";
-			getline(cin, input);
-			if (cin.eof()) { input = "quit()"; }
+
+			mout->mothurOutEndLine();
+			
+			input = getCommand();	
+			mout->mothurOutEndLine();	
+		
+			if (mout->control_pressed) { input = "quit()"; }
 			
 			//allow user to omit the () on the quit command
 			if (input == "quit") { input = "quit()"; }
 			
-			//errorFree = errorCheckor->checkInput(input);
-			//if (errorFree == true) {
 			CommandOptionParser parser(input);
 			commandName = parser.getCommandString();
+	
 			options = parser.getOptionString();
 			
 			if (commandName != "") {
-			
-				//executes valid command
-				CommandFactory cFactory;
-				Command* command = cFactory.getCommand(commandName, options);
-				quitCommandCalled = command->execute();
-				
-			}else {
-				cout << "Your input contains errors. Please try again." << endl;
-			}
+					mout->executing = true;
+					#ifdef USE_MPI
+						int pid;
+						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+ 
+//cout << pid << " is here " << commandName << endl;
+						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+					#endif
+					//executes valid command
+					Command* command = cFactory->getCommand(commandName, options);
+					quitCommandCalled = command->execute();
+					mout->control_pressed = 0;
+					mout->executing = false;
+										
+					#ifdef USE_MPI
+						}
+					#endif
+				}else {		
+					mout->mothurOut("Invalid."); 
+					mout->mothurOutEndLine();
+				}
 		}	
 		return 1;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the InteractEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		mout->errorOut(e, "InteractEngine", "getInput");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the InteractEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/***********************************************************************/
+string Engine::getCommand()  {
+	try {
+		#ifdef USE_MPI
+			MPI_Barrier(MPI_COMM_WORLD);
+		#endif
+	
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			#ifdef USE_READLINE
+				char* nextCommand = NULL;
+				nextCommand = readline("mothur > ");
+				
+				if(nextCommand != NULL) {  add_history(nextCommand);  }	
+				else{ //^D causes null string and we want it to quit mothur
+					nextCommand = "quit"; 
+					mout->mothurOut(nextCommand);
+				}	
+				
+				mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
+				return nextCommand;
+			#else
+				string nextCommand = "";
+				mout->mothurOut("mothur > ");
+				getline(cin, nextCommand);
+				mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
+				
+				return nextCommand;
+			#endif
+		#else
+				string nextCommand = "";
+				
+				mout->mothurOut("mothur > ");
+				getline(cin, nextCommand);
+				mout->mothurOutJustToLog(toString(nextCommand));
+				
+				return nextCommand;
+		#endif
+	
+						
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "Engine", "getCommand");
 		exit(1);
 	}
-
 }
-
 /***********************************************************************/
 //This function opens the batchfile to be used by BatchEngine::getInput.
 BatchEngine::BatchEngine(string path, string batchFileName){
 	try {
 		globaldata = GlobalData::getInstance();
+	
 		openedBatch = openInputFile(batchFileName, inputBatchFile);
 		globaldata->argv = path;
-
-		system("clear");
-	
-	//	char buffer = ' ';
-	//	ifstream header("introtext.txt");
-	//	while(!header.eof()){
-	//		cout << buffer;
-	//		buffer = header.get();
-	//	}
+				
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the BatchEngine class function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		mout->errorOut(e, "BatchEngine", "BatchEngine");
 		exit(1);
 	}
 }
 
 /***********************************************************************/
 
-BatchEngine::~BatchEngine(){
-	}
+BatchEngine::~BatchEngine(){	}
 
 /***********************************************************************/
 //This Function allows the user to run a batchfile containing several commands on Dotur
 bool BatchEngine::getInput(){
 	try {
 		//check if this is a valid batchfile
-		if (openedBatch == 1) {  cout << "unable to open batchfile" << endl;  return 1; }
+		if (openedBatch == 1) {  
+			mout->mothurOut("unable to open batchfile");  
+			mout->mothurOutEndLine();
+			return 1; 
+		}
 	
 		string input = "";
 		string commandName = "";
@@ -143,15 +179,19 @@ bool BatchEngine::getInput(){
 		
 		//CommandFactory cFactory;
 		int quitCommandCalled = 0;
-	
+	    int count = 0;
 		while(quitCommandCalled == 0){
-		
-			if (inputBatchFile.eof()) { input = "quit()"; }
-			else { getline(inputBatchFile, input); }
+	
+			input = getNextCommand(inputBatchFile);
+			count++;
 			
 			if (input[0] != '#') {
-			
-				cout << endl << "mothur > " << input << endl;
+				
+				mout->mothurOutEndLine();
+				mout->mothurOut("mothur > " + input);
+				mout->mothurOutEndLine();
+							
+				if (mout->control_pressed) { input = "quit()"; }
 				
 				//allow user to omit the () on the quit command
 				if (input == "quit") { input = "quit()"; }
@@ -161,28 +201,193 @@ bool BatchEngine::getInput(){
 				options = parser.getOptionString();
 										
 				if (commandName != "") {
-
+					mout->executing = true;
+					#ifdef USE_MPI
+						int pid;
+						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+						
+//cout << pid << " is here " << commandName << '\t' << count << endl;
+						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+					#endif
 					//executes valid command
-					CommandFactory cFactory;
-					Command* command = cFactory.getCommand(commandName, options);
+					Command* command = cFactory->getCommand(commandName, options);
 					quitCommandCalled = command->execute();
-				}else {		cout << "Invalid." << endl;		}
+					mout->control_pressed = 0;
+					mout->executing = false;
+										
+					#ifdef USE_MPI
+						}
+					#endif
+				}else {		
+					mout->mothurOut("Invalid."); 
+					mout->mothurOutEndLine();
+				}
 				
 			}
 			gobble(inputBatchFile);
 		}
+		
+		inputBatchFile.close();
 		return 1;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		mout->errorOut(e, "BatchEngine", "getInput");
+		exit(1);
+	}
+}
+/***********************************************************************/
+string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
+	try {
+		
+		#ifdef USE_MPI
+			int err = MPI_Barrier(MPI_COMM_WORLD);
+//cout << "barrier = " << err << '\t' << MPI_SUCCESS << endl;
+		#endif
+		
+		string nextcommand = "";
+		
+		if (inputBatchFile.eof()) { nextcommand = "quit()"; }
+		else { nextcommand = getline(inputBatchFile); }
+		
+		return nextcommand;
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "BatchEngine", "getNextCommand");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the BatchEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+/***********************************************************************/
+/***********************************************************************/
+//This function opens the batchfile to be used by BatchEngine::getInput.
+ScriptEngine::ScriptEngine(string path, string commandString){
+	try {
+		globaldata = GlobalData::getInstance();
+		
+		//remove quotes
+		listOfCommands = commandString.substr(1, (commandString.length()-1));
+
+		globaldata->argv = path;
+				
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "ScriptEngine", "ScriptEngine");
 		exit(1);
 	}
 }
 
+/***********************************************************************/
+
+ScriptEngine::~ScriptEngine(){ 	}
 
 /***********************************************************************/
+//This Function allows the user to run a batchfile containing several commands on mothur
+bool ScriptEngine::getInput(){
+	try {
+			
+		string input = "";
+		string commandName = "";
+		string options = "";
+		
+		
+		//CommandFactory cFactory;
+		int quitCommandCalled = 0;
+	
+		while(quitCommandCalled == 0){
+		
+			input = getNextCommand(listOfCommands);	
+			
+			if (input == "") { input = "quit()"; }
+			
+			mout->mothurOutEndLine();
+			mout->mothurOut("mothur > " + input);
+			mout->mothurOutEndLine();
+			
+			if (mout->control_pressed) { input = "quit()"; }
+				
+			//allow user to omit the () on the quit command
+			if (input == "quit") { input = "quit()"; }
+
+			CommandOptionParser parser(input);
+			commandName = parser.getCommandString();
+			options = parser.getOptionString();
+										
+			if (commandName != "") {
+					mout->executing = true;
+					#ifdef USE_MPI
+						int pid, numProcesses;
+						MPI_Status status; 
+						
+						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+						MPI_Comm_size(MPI_COMM_WORLD, &numProcesses); 
+					
+//cout << pid << " is here " << commandName  << endl;
+						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+							//cout << pid << " is in execute" << endl;	
+					#endif
+					//executes valid command
+					Command* command = cFactory->getCommand(commandName, options);
+					quitCommandCalled = command->execute();
+					mout->control_pressed = 0;
+					mout->executing = false;
+									
+					#ifdef USE_MPI
+					//cout << pid << " is done in execute" << endl;
+						}
+					#endif
+				}else {		
+					mout->mothurOut("Invalid."); 
+					mout->mothurOutEndLine();
+				}
 
+			
+		}
+		
+		return 1;
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "ScriptEngine", "getInput");
+		exit(1);
+	}
+}
+/***********************************************************************/
+string ScriptEngine::getNextCommand(string& commandString) {
+	try {
+		
+		#ifdef USE_MPI
+			MPI_Barrier(MPI_COMM_WORLD);
+		#endif
+		
+		string nextcommand = "";
+		int count = 0;
+		
+		//go through string until you reach ; or end
+		while (count < commandString.length()) { 
+			
+			if (commandString[count] == ';') {  break;   }
+			else {		nextcommand += commandString[count];	}
+			
+			count++;
+		}
+		
+		//if you are not at the end
+		if (count != commandString.length())  {   commandString = commandString.substr(count+1, commandString.length());  }
+		else { commandString = ""; }
+				
+		
+		//get rid of spaces in between commands if any
+		if (commandString.length() > 0) {
+			while (commandString[0] == ' ') {  
+				commandString = commandString.substr(1,commandString.length());
+				if (commandString.length() == 0) {  break;  }
+			}
+		}
+		
+		return nextcommand;
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "ScriptEngine", "getNextCommand");
+		exit(1);
+	}
+}
+/***********************************************************************/